The Proteomics Core enhances the research productivity of KCI members by providing the equipment and trained personnel necessary for analysis of cellular protein composition, protein modification, protein quantitation and protein interaction. Proteome profiling and protein identification services utilize modern mass spectrometer based methods. The primary platform for analysis is the Thermo Finnigan LTQ Linear lon Trap equipped with Electron Transfer Dissociation (ETD). Isolated protein, gel plug and full proteome analysis are supported. Sample preparation is achieved by robotic or manual depletion of high abundance proteins, digestion and solid phase extraction (SPE). Various sorbents including specialized sorbents such as Ti02 for isolation of phosphopeptides are available for SPE. Nanoflow HPLC from a Michrom H4 platform is utilized for most analyses with a Triversa Nanomate robot available as needed. Data analysis is achieved using Mascot, Sequest, XITandem and PEAKS algorithms with secondary data analysis by Scaffold. Results are distributed as hard copy on CD or by deposition on the international Tranche network. The Core enhances research productivity by providing a clear and easily accessible mechanism for protein identification and for relative quantitation of proteins based on isobaric tags. Quantitation technologies supported include cICAT, ITraq, TMT and SILAC and Multiple Reaction Monitoring (MRM). Analysis of isotopically labeled samples is achieved using the Mascot Quantitation package. MRM analysis is achieved using the TSQ Vantage with PinPoint and Skyline software for experimental design and data analysis. The protein identification component of the Proteomics Core provides KCI members access to technology for protein identification, proteomic profiling and biomarker identification. The protein interactions component of the Core provides instrumentation and services for detection of protein binding by Fluorescence Polarization (FP) and Surface Plasmon Resonance (SPR). The instruments in the Core produce sensitive, accurate and real time measurements of protein binding events. Thus, the protein interactions component of the Core supports investigators in asking questions about protein-protein interactions and the effects of those interactions on signaling pathways and cellular function.